# Diversity Estimation of a metacommunity

### Description

Estimates diversity of a metacommunity.

### Usage

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### Arguments

`q` |
A number: the order of diversity. |

`MC` |
A |

`Biased` |
Logical; if |

`Correction` |
A string containing one of the possible corrections. The correction must be accepted by |

`Tree` |
An object of class |

`Normalize` |
If |

`Z` |
A relatedness matrix, |

`Simulations` |
The number of simulations to build confidence intervals. |

`CheckArguments` |
Logical; if |

`x` |
An object to be tested or plotted. |

`main` |
The title of the plot. |

`Which` |
May be |

`object` |
A |

`...` |
Additional arguments to be passed to the generic methods. |

### Details

`Divest`

estimates the diversity of the metacommunity and partitions it into alpha and beta components.

If `Tree`

is provided, the phylogenetic diversity is calculated else if `Z`

is not `NULL`

, then similarity-based entropy is calculated.

Bootstrap confidence intervals are calculated by drawing simulated communities from a multinomial distribution following the observed frequencies (Marcon et al, 2012; 2014).

### Value

A `Divest`

object which is a `DivPart`

object with an additional item in its list:

`SimulatedDiversity` |
A matrix containing the simulated values of alpha, beta and gamma diversity. |

`Divest`

objects can be summarized and plotted.

### Author(s)

Eric Marcon <Eric.Marcon@ecofog.gf> and Bruno Herault <Bruno.Herault@ecofog.gf>

### References

Marcon, E., Herault, B., Baraloto, C. and Lang, G. (2012). The Decomposition of Shannon's Entropy and a Confidence Interval for Beta Diversity. *Oikos* 121(4): 516-522.

Marcon, E., Scotti, I., Herault, B., Rossi, V. and Lang, G. (2014). Generalization of the partitioning of Shannon diversity. *PLOS One* 9(3): e90289.

Marcon, E., Herault, B. (2015). Decomposing Phylodiversity. *Methods in Ecology and Evolution* 6(3): 333-339.

### See Also

`DivPart`

### Examples

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